Example 1 with DivideByZeroException
use of cbit.vcell.parser.DivideByZeroException in project vcell by virtualcell.
the class ODETimePlotMultipleScansPanel method initialize.
/**
* Insert the method's description here.
* Creation date: (10/17/2005 11:37:52 PM)
* @exception org.vcell.util.DataAccessException The exception description.
*/
private void initialize() {
setLayout(new BorderLayout());
int scanCount = simulation.getScanCount();
plotPane = new PlotPane();
add(plotPane, BorderLayout.CENTER);
JPanel parameterPanel = new JPanel();
parameterPanel.setLayout(new BorderLayout());
JLabel label = new JLabel();
label.setHorizontalAlignment(SwingConstants.CENTER);
label.setText("<html><b><u>Choose one or more Parameter Value Sets </u></b></html>");
label.setBorder(BorderFactory.createEmptyBorder(10, 4, 10, 4));
parameterPanel.add(label, BorderLayout.NORTH);
String[] scanParams = simulation.getMathOverrides().getScannedConstantNames();
Arrays.sort(scanParams);
class ScanChoicesTableModel extends javax.swing.table.AbstractTableModel {
String[] columnNames;
Double[][] rowData;
ScanChoicesTableModel(Double[][] argData, String[] argNames) {
columnNames = argNames;
rowData = argData;
}
public String getColumnName(int column) {
if (column == 0) {
return JOB_PLOT_NAME;
}
return columnNames[column - 1].toString();
}
public int getRowCount() {
return rowData.length;
}
public int getColumnCount() {
return columnNames.length + 1;
}
public Object getValueAt(int row, int col) {
if (col == 0) {
return new Integer(row);
}
return rowData[row][col - 1];
}
@Override
public boolean isCellEditable(int row, int column) {
return false;
}
@Override
public Class<?> getColumnClass(int columnIndex) {
return Number.class;
}
}
;
Double[][] values = new Double[scanCount][scanParams.length];
for (int i = 0; i < scanCount; i++) {
for (int j = 0; j < scanParams.length; j++) {
Expression scanConstantExp = simulation.getMathOverrides().getActualExpression(scanParams[j], i);
try {
values[i][j] = scanConstantExp.evaluateConstant();
} catch (DivideByZeroException e1) {
e1.printStackTrace();
} catch (ExpressionException e1) {
e1.printStackTrace();
}
}
}
ScanChoicesTableModel tm = new ScanChoicesTableModel(values, scanParams);
scanChoiceTable = new JTable(tm);
scanChoiceTable.setSelectionMode(ListSelectionModel.MULTIPLE_INTERVAL_SELECTION);
JScrollPane scr = new JScrollPane(scanChoiceTable, JScrollPane.VERTICAL_SCROLLBAR_ALWAYS, JScrollPane.HORIZONTAL_SCROLLBAR_ALWAYS);
scr.setPreferredSize(new java.awt.Dimension(100, Math.min(150, scanChoiceTable.getPreferredSize().height + scanChoiceTable.getTableHeader().getPreferredSize().height + 5)));
parameterPanel.add(scr, BorderLayout.CENTER);
parameterPanel.setBorder(BorderFactory.createEtchedBorder());
TableColumn col = scanChoiceTable.getColumnModel().getColumn(0);
int width = 50;
col.setMinWidth(width);
col.setMaxWidth(width);
col.setPreferredWidth(width);
// put things together
add(parameterPanel, BorderLayout.SOUTH);
scanChoiceTable.getSelectionModel().addListSelectionListener(new javax.swing.event.ListSelectionListener() {
public void valueChanged(javax.swing.event.ListSelectionEvent e) {
if (!e.getValueIsAdjusting()) {
updateScanParamChoices();
}
}
});
// scanChoiceTable.getSelectionModel().setSelectionInterval(0,0);
}
Also used :
JPanel(javax.swing.JPanel)
ExpressionException(cbit.vcell.parser.ExpressionException)
DivideByZeroException(cbit.vcell.parser.DivideByZeroException)
BorderLayout(java.awt.BorderLayout)
JScrollPane(javax.swing.JScrollPane)
JLabel(javax.swing.JLabel)
TableColumn(javax.swing.table.TableColumn)
Expression(cbit.vcell.parser.Expression)
JTable(javax.swing.JTable)
PlotPane(cbit.plot.gui.PlotPane)
Example 2 with DivideByZeroException
use of cbit.vcell.parser.DivideByZeroException in project vcell by virtualcell.
the class RowColumnResultSet method extractColumn.
/**
* getVariableNames method comment.
* If column is empty, return null or an empty array?
* For now, null...
*/
public synchronized double[] extractColumn(int c) throws ExpressionException {
double[] values = null;
if (getRowCount() > 0) {
ColumnDescription colDescription = getColumnDescriptions(c);
if (colDescription instanceof FunctionColumnDescription) {
Expression exp = ((FunctionColumnDescription) colDescription).getExpression();
//
// must rebind expression due to transient nature of expression binding (see ASTIdNode.symbolTableEntry)
//
exp.bindExpression(getResultSetSymbolTableWithoutFunction());
values = new double[getRowCount()];
for (int r = 0; r < getRowCount(); r++) {
try {
values[r] = exp.evaluateVector(getRow(r));
} catch (DivideByZeroException e) {
e.printStackTrace(System.out);
values[r] = Double.NaN;
} catch (FunctionDomainException e) {
e.printStackTrace(System.out);
values[r] = Double.NaN;
}
}
} else {
values = new double[getRowCount()];
for (int r = 0; r < getRowCount(); r++) {
values[r] = getRow(r)[c];
}
}
}
return (values);
}
Also used :
DivideByZeroException(cbit.vcell.parser.DivideByZeroException)
Expression(cbit.vcell.parser.Expression)
FunctionDomainException(cbit.vcell.parser.FunctionDomainException)
ColumnDescription(cbit.vcell.util.ColumnDescription)
Example 3 with DivideByZeroException
use of cbit.vcell.parser.DivideByZeroException in project vcell by virtualcell.
the class DataSetControllerImpl method evaluateFunction.
/**
* Insert the method's description here.
* Creation date: (10/13/00 9:13:52 AM)
* @return cbit.vcell.simdata.SimDataBlock
* @param user cbit.vcell.server.User
* @param simResults cbit.vcell.simdata.SimResults
* @param function cbit.vcell.math.Function
* @param time double
*/
private SimDataBlock evaluateFunction(OutputContext outputContext, final VCDataIdentifier vcdID, VCData simData, AnnotatedFunction function, double time) throws ExpressionException, DataAccessException, IOException, MathException {
Expression exp = new Expression(function.getExpression());
exp = SolverUtilities.substituteSizeAndNormalFunctions(exp, function.getFunctionType().getVariableDomain());
exp.bindExpression(simData);
exp = fieldFunctionSubstitution(outputContext, vcdID, exp);
//
// get Dependent datasets
//
// variables are indexed by a number, t=0, x=1, y=2, z=3, a(i) = 4+i where a's are other variables
// these variables
//
CartesianMesh mesh = null;
if (function.getFunctionType().equals(VariableType.POSTPROCESSING)) {
mesh = ((SimulationData) simData).getPostProcessingMesh(function.getName(), outputContext);
}
if (mesh == null) {
mesh = getMesh(vcdID);
}
String[] dependentIDs = exp.getSymbols();
Vector<SimDataHolder> dataSetList = new Vector<SimDataHolder>();
Vector<DataSetIdentifier> dependencyList = new Vector<DataSetIdentifier>();
int varIndex = TXYZ_OFFSET;
int dataLength = 0;
long lastModified = 0;
VariableType variableType = function.getFunctionType();
if (variableType.equals(VariableType.VOLUME) || variableType.equals(VariableType.POSTPROCESSING)) {
dataLength = mesh.getNumVolumeElements();
} else if (variableType.equals(VariableType.MEMBRANE)) {
dataLength = mesh.getNumMembraneElements();
} else if (variableType.equals(VariableType.VOLUME_REGION)) {
dataLength = mesh.getNumVolumeRegions();
} else if (variableType.equals(VariableType.MEMBRANE_REGION)) {
dataLength = mesh.getNumMembraneRegions();
}
VariableType computedVariableType = null;
int computedDataLength = 0;
for (int i = 0; dependentIDs != null && i < dependentIDs.length; i++) {
SymbolTableEntry ste = exp.getSymbolBinding(dependentIDs[i]);
if (ste instanceof DataSetIdentifier) {
DataSetIdentifier dsi = (DataSetIdentifier) ste;
dependencyList.addElement(dsi);
dsi.setIndex(varIndex++);
if (dsi.getName().endsWith(OutsideVariable.OUTSIDE_VARIABLE_SUFFIX) || dsi.getName().endsWith(InsideVariable.INSIDE_VARIABLE_SUFFIX)) {
String volVarName = dsi.getName().substring(0, dsi.getName().lastIndexOf("_"));
SimDataBlock simDataBlock = getSimDataBlock(outputContext, vcdID, volVarName, time);
lastModified = simDataBlock.getPDEDataInfo().getTimeStamp();
//
if (simDataBlock.getVariableType().equals(VariableType.VOLUME)) {
computedVariableType = VariableType.MEMBRANE;
computedDataLength = mesh.getMembraneElements().length;
//
// if inside/outside volume element dependent, then can only be a membrane type
//
} else if (simDataBlock.getVariableType().equals(VariableType.VOLUME_REGION) && variableType == null) {
computedVariableType = VariableType.MEMBRANE_REGION;
computedDataLength = mesh.getNumMembraneRegions();
}
dataSetList.addElement(simDataBlock);
} else {
SimDataBlock simDataBlock = getSimDataBlock(outputContext, vcdID, dsi.getName(), time);
if (variableType == null || simDataBlock.getVariableType().isExpansionOf(variableType)) {
lastModified = simDataBlock.getPDEDataInfo().getTimeStamp();
computedDataLength = simDataBlock.getData().length;
computedVariableType = simDataBlock.getVariableType();
}
dataSetList.addElement(simDataBlock);
}
} else if (ste instanceof ReservedVariable) {
ReservedVariable rv = (ReservedVariable) ste;
if (rv.isTIME()) {
rv.setIndex(0);
} else if (rv.isX()) {
rv.setIndex(1);
} else if (rv.isY()) {
rv.setIndex(2);
} else if (rv.isZ()) {
rv.setIndex(3);
}
} else if (ste instanceof FieldDataParameterVariable) {
// Field Data
((FieldDataParameterVariable) ste).setIndex(varIndex++);
final double[] steResampledFieldData = ((FieldDataParameterVariable) ste).getResampledFieldData();
final VariableType newVariableType = (steResampledFieldData.length == mesh.getNumVolumeElements() ? VariableType.VOLUME : (steResampledFieldData.length == mesh.getNumMembraneElements() ? VariableType.MEMBRANE : null));
if (newVariableType == null) {
throw new DataAccessException("Couldn't determine VariableType for FieldData");
}
if (variableType != null && !variableType.equals(newVariableType)) {
throw new DataAccessException("Incompatible VariableType for FieldData");
}
SimDataHolder newSimDataHolder = new SimDataHolder() {
public double[] getData() {
return steResampledFieldData;
}
public VariableType getVariableType() {
return newVariableType;
}
};
dataSetList.addElement(newSimDataHolder);
dependencyList.add(new DataSetIdentifier(ste.getName(), newVariableType, ((FieldDataParameterVariable) ste).getDomain()));
if (variableType == null) {
computedVariableType = newVariableType;
computedDataLength = newSimDataHolder.getData().length;
}
}
}
if (computedDataLength <= 0) {
if (lg.isWarnEnabled())
lg.warn("dependencies for function '" + function + "' not found, assuming datalength of volume");
computedDataLength = mesh.getDataLength(VariableType.VOLUME);
computedVariableType = VariableType.VOLUME;
// try {
// computedDataLength = mesh.getDataLength(VariableType.VOLUME);
// computedVariableType = VariableType.VOLUME;
// }catch (MathException e){
// lg.error(e.getMessage(), e);
// throw new RuntimeException("MathException, cannot determine domain for function '"+function+"'");
// }catch (FileNotFoundException e){
// lg.error(e.getMessage(), e);
// throw new RuntimeException("Mesh not found, cannot determine domain for function '"+function+"'");
// }
}
if (!variableType.equals(computedVariableType)) {
System.err.println("function [" + function.getName() + "] variable type [" + variableType.getTypeName() + "] is not equal to computed variable type [" + computedVariableType.getTypeName() + "].");
}
if (dataLength == 0) {
dataLength = computedDataLength;
variableType = computedVariableType;
}
//
// Gradient Info for special processing
//
boolean isGrad = hasGradient(exp);
if (isGrad && !variableType.equals(VariableType.VOLUME)) {
throw new DataAccessException("Gradient function is not implemented for datatype " + variableType.getTypeName());
}
double[] args = new double[varIndex + (isGrad ? 12 * varIndex : 0)];
double[] data = new double[dataLength];
// time
args[0] = time;
// x
args[1] = 0.0;
// y
args[2] = 0.0;
// z
args[3] = 0.0;
String dividedByZeroMsg = "";
for (int i = 0; i < dataLength; i++) {
//
if (variableType.equals(VariableType.VOLUME) || variableType.equals(VariableType.POSTPROCESSING)) {
Coordinate coord = mesh.getCoordinateFromVolumeIndex(i);
args[1] = coord.getX();
args[2] = coord.getY();
args[3] = coord.getZ();
for (int j = 0; j < varIndex - TXYZ_OFFSET; j++) {
SimDataHolder simDataHolder = dataSetList.elementAt(j);
if (simDataHolder.getVariableType().equals(VariableType.VOLUME) || simDataHolder.getVariableType().equals(VariableType.POSTPROCESSING)) {
args[TXYZ_OFFSET + j] = simDataHolder.getData()[i];
} else if (simDataHolder.getVariableType().equals(VariableType.VOLUME_REGION)) {
int volumeIndex = mesh.getVolumeRegionIndex(i);
args[TXYZ_OFFSET + j] = simDataHolder.getData()[volumeIndex];
} else if (simDataHolder.getVariableType().equals(VariableType.POINT_VARIABLE)) {
args[TXYZ_OFFSET + j] = simDataHolder.getData()[0];
}
}
if (isGrad) {
getSpatialNeighborData(mesh, i, varIndex, time, dataSetList, args);
}
} else if (variableType.equals(VariableType.VOLUME_REGION)) {
for (int j = 0; j < varIndex - TXYZ_OFFSET; j++) {
SimDataHolder simDataHolder = dataSetList.elementAt(j);
if (simDataHolder.getVariableType().equals(VariableType.VOLUME_REGION)) {
args[TXYZ_OFFSET + j] = simDataHolder.getData()[i];
} else if (simDataHolder.getVariableType().equals(VariableType.POINT_VARIABLE)) {
args[TXYZ_OFFSET + j] = simDataHolder.getData()[0];
}
}
} else if (variableType.equals(VariableType.MEMBRANE)) {
Coordinate coord = mesh.getCoordinateFromMembraneIndex(i);
args[1] = coord.getX();
args[2] = coord.getY();
args[3] = coord.getZ();
for (int j = 0; j < varIndex - TXYZ_OFFSET; j++) {
DataSetIdentifier dsi = (DataSetIdentifier) dependencyList.elementAt(j);
SimDataHolder simDataHolder = dataSetList.elementAt(j);
if (simDataHolder.getVariableType().equals(VariableType.VOLUME)) {
if (mesh.isChomboMesh()) {
String varName = dsi.getName();
if (dsi.getName().endsWith(InsideVariable.INSIDE_VARIABLE_SUFFIX)) {
varName = varName.substring(0, varName.lastIndexOf(InsideVariable.INSIDE_VARIABLE_SUFFIX));
} else if (dsi.getName().endsWith(OutsideVariable.OUTSIDE_VARIABLE_SUFFIX)) {
varName = varName.substring(0, varName.lastIndexOf(OutsideVariable.OUTSIDE_VARIABLE_SUFFIX));
}
args[TXYZ_OFFSET + j] = getChomboExtrapolatedValues(vcdID, varName, time).getData()[i];
} else {
if (dsi.getName().endsWith(InsideVariable.INSIDE_VARIABLE_SUFFIX)) {
args[TXYZ_OFFSET + j] = interpolateVolDataValToMemb(mesh, i, simDataHolder, true, false);
} else if (dsi.getName().endsWith(OutsideVariable.OUTSIDE_VARIABLE_SUFFIX)) {
args[TXYZ_OFFSET + j] = interpolateVolDataValToMemb(mesh, i, simDataHolder, false, false);
} else {
args[TXYZ_OFFSET + j] = interpolateVolDataValToMemb(mesh, dsi.getDomain(), i, simDataHolder, false);
}
}
} else if (simDataHolder.getVariableType().equals(VariableType.VOLUME_REGION)) {
if (dsi.getName().endsWith(InsideVariable.INSIDE_VARIABLE_SUFFIX)) {
args[TXYZ_OFFSET + j] = interpolateVolDataValToMemb(mesh, i, simDataHolder, true, true);
} else if (dsi.getName().endsWith(OutsideVariable.OUTSIDE_VARIABLE_SUFFIX)) {
args[TXYZ_OFFSET + j] = interpolateVolDataValToMemb(mesh, i, simDataHolder, false, true);
} else {
args[TXYZ_OFFSET + j] = interpolateVolDataValToMemb(mesh, dsi.getDomain(), i, simDataHolder, true);
}
} else if (simDataHolder.getVariableType().equals(VariableType.MEMBRANE)) {
args[TXYZ_OFFSET + j] = simDataHolder.getData()[i];
} else if (simDataHolder.getVariableType().equals(VariableType.MEMBRANE_REGION)) {
int memRegionIndex = mesh.getMembraneRegionIndex(i);
args[TXYZ_OFFSET + j] = simDataHolder.getData()[memRegionIndex];
} else if (simDataHolder.getVariableType().equals(VariableType.POINT_VARIABLE)) {
args[TXYZ_OFFSET + j] = simDataHolder.getData()[0];
}
}
} else if (variableType.equals(VariableType.MEMBRANE_REGION)) {
for (int j = 0; j < varIndex - TXYZ_OFFSET; j++) {
DataSetIdentifier dsi = (DataSetIdentifier) dependencyList.elementAt(j);
SimDataHolder simDataHolder = dataSetList.elementAt(j);
if (simDataHolder.getVariableType().equals(VariableType.VOLUME_REGION) && dsi.getName().endsWith(InsideVariable.INSIDE_VARIABLE_SUFFIX)) {
//
for (int k = 0; k < mesh.getMembraneElements().length; k++) {
if (mesh.getMembraneRegionIndex(k) == i) {
args[TXYZ_OFFSET + j] = interpolateVolDataValToMemb(mesh, i, simDataHolder, true, true);
break;
}
}
} else if (simDataHolder.getVariableType().equals(VariableType.VOLUME_REGION) && dsi.getName().endsWith(OutsideVariable.OUTSIDE_VARIABLE_SUFFIX)) {
//
for (int k = 0; k < mesh.getMembraneElements().length; k++) {
if (mesh.getMembraneRegionIndex(k) == i) {
args[TXYZ_OFFSET + j] = interpolateVolDataValToMemb(mesh, i, simDataHolder, false, true);
break;
}
}
} else if (simDataHolder.getVariableType().equals(VariableType.MEMBRANE)) {
args[TXYZ_OFFSET + j] = simDataHolder.getData()[i];
} else if (simDataHolder.getVariableType().equals(VariableType.MEMBRANE_REGION)) {
int memRegionIndex = i;
args[TXYZ_OFFSET + j] = simDataHolder.getData()[memRegionIndex];
} else if (simDataHolder.getVariableType().equals(VariableType.POINT_VARIABLE)) {
args[TXYZ_OFFSET + j] = simDataHolder.getData()[0];
}
}
}
try {
data[i] = exp.evaluateVector(args);
// if(time ==0){
// System.out.print("non-multi evalFunction ");
// for (int m = 0; m < args.length; m++) {
// System.out.print(args[m]);
// }
// System.out.println(" "+(args[args.length-2]/args[args.length-1]));
// }
} catch (DivideByZeroException e) {
dividedByZeroMsg = e.getMessage();
data[i] = Double.POSITIVE_INFINITY;
}
}
if (dividedByZeroMsg.length() != 0) {
System.out.println("DataSetControllerImpl.evaluateFunction(): DivideByZero " + dividedByZeroMsg);
}
PDEDataInfo pdeDataInfo = new PDEDataInfo(vcdID.getOwner(), vcdID.getID(), function.getName(), time, lastModified);
return new SimDataBlock(pdeDataInfo, data, variableType);
}
Also used :
VariableType(cbit.vcell.math.VariableType)
DivideByZeroException(cbit.vcell.parser.DivideByZeroException)
CartesianMesh(cbit.vcell.solvers.CartesianMesh)
SymbolTableEntry(cbit.vcell.parser.SymbolTableEntry)
ReservedVariable(cbit.vcell.math.ReservedVariable)
Expression(cbit.vcell.parser.Expression)
Coordinate(org.vcell.util.Coordinate)
Vector(java.util.Vector)
DataAccessException(org.vcell.util.DataAccessException)
FieldDataParameterVariable(cbit.vcell.field.FieldDataParameterVariable)
Example 4 with DivideByZeroException
use of cbit.vcell.parser.DivideByZeroException in project vcell by virtualcell.
the class SmoldynFileWriter method writeRuntimeCommands.
// uncomment for debug
/*private void writeGraphicsLegend() throws MathException{
try {
java.awt.image.BufferedImage cmapImage = new java.awt.image.BufferedImage(200, particleVariableList.size()*30,java.awt.image.BufferedImage.TYPE_INT_RGB);
Graphics g = cmapImage.getGraphics();
for (int i = 0; i < particleVariableList.size(); i ++) {
Color c = colors[i];
System.out.println("color for legend: " + "red--"+ c.getRed() + " green--" + c.getGreen() + " blue--" + c.getBlue());
String variableName = getVariableName(particleVariableList.get(i),null);
g.setColor(c);
g.drawString(variableName, 5, 30*i + 20);
g.fillRect(105, 30*i + 10, 20, 10);
}
g.dispose();
File tmpFile = File.createTempFile("legend", ".jpg");
FileOutputStream fios = null;
try {
printWriter.println("# legend file: " + tmpFile.getAbsolutePath());
fios = new FileOutputStream(tmpFile);
ImageIO.write(cmapImage,"jpg",fios);
} finally {
if(fios != null) {fios.close();}
}
} catch (Exception e) {
e.printStackTrace();
throw new MathException(e.getMessage());
}
}*/
private void writeRuntimeCommands() throws SolverException, DivideByZeroException, DataAccessException, IOException, MathException, ExpressionException {
printWriter.println("# " + SmoldynVCellMapper.SmoldynKeyword.killmolincmpt + " runtime command to kill molecules misplaced during initial condtions");
for (ParticleVariable pv : particleVariableList) {
CompartmentSubDomain varDomain = mathDesc.getCompartmentSubDomain(pv.getDomain().getName());
if (varDomain == null) {
continue;
}
boolean bkillMol = false;
ArrayList<ParticleInitialCondition> iniConditionList = varDomain.getParticleProperties(pv).getParticleInitialConditions();
for (ParticleInitialCondition iniCon : iniConditionList) {
if (iniCon instanceof ParticleInitialConditionConcentration) {
try {
subsituteFlattenToConstant(((ParticleInitialConditionConcentration) iniCon).getDistribution());
} catch (// can not be evaluated to a constant
Exception e) {
bkillMol = true;
break;
}
}
}
if (bkillMol) {
Enumeration<SubDomain> subDomainEnumeration = mathDesc.getSubDomains();
while (subDomainEnumeration.hasMoreElements()) {
SubDomain subDomain = subDomainEnumeration.nextElement();
if (subDomain instanceof CompartmentSubDomain && varDomain != subDomain) {
printWriter.println(SmoldynVCellMapper.SmoldynKeyword.cmd + " " + SmoldynVCellMapper.SmoldynKeyword.B + " " + SmoldynVCellMapper.SmoldynKeyword.killmolincmpt + " " + pv.getName() + "(" + SmoldynVCellMapper.SmoldynKeyword.all + ") " + subDomain.getName());
}
}
}
}
printWriter.println();
// write command to kill molecules on membrane for adsortption to nothing
printWriter.println("# kill membrane molecues that are absorbed (to nothing)");
for (String killMolCmd : killMolCommands) {
printWriter.println(killMolCmd);
}
printWriter.println();
printWriter.println("# runtime command");
printWriter.println(SmoldynVCellMapper.SmoldynKeyword.cmd + " " + SmoldynVCellMapper.SmoldynKeyword.E + " " + VCellSmoldynKeyword.vcellPrintProgress);
if (outputFile != null && cartesianMesh != null) {
OutputTimeSpec ots = simulation.getSolverTaskDescription().getOutputTimeSpec();
if (ots.isUniform()) {
printWriter.println(SmoldynVCellMapper.SmoldynKeyword.output_files + " " + outputFile.getName());
ISize sampleSize = simulation.getMeshSpecification().getSamplingSize();
TimeStep timeStep = simulation.getSolverTaskDescription().getTimeStep();
int n = (int) Math.round(((UniformOutputTimeSpec) ots).getOutputTimeStep() / timeStep.getDefaultTimeStep());
if (simulation.getSolverTaskDescription().getSmoldynSimulationOptions().isSaveParticleLocations()) {
printWriter.println(SmoldynVCellMapper.SmoldynKeyword.cmd + " " + SmoldynVCellMapper.SmoldynKeyword.N + " " + n + " " + SmoldynVCellMapper.SmoldynKeyword.incrementfile + " " + outputFile.getName());
printWriter.println(SmoldynVCellMapper.SmoldynKeyword.cmd + " " + SmoldynVCellMapper.SmoldynKeyword.N + " " + n + " " + SmoldynVCellMapper.SmoldynKeyword.listmols + " " + outputFile.getName());
}
// DON'T CHANGE THE ORDER HERE.
// DataProcess must be before vcellWriteOutput
writeDataProcessor();
printWriter.println(SmoldynVCellMapper.SmoldynKeyword.cmd + " " + SmoldynVCellMapper.SmoldynKeyword.N + " " + n + " " + VCellSmoldynKeyword.vcellWriteOutput + " begin");
printWriter.println(SmoldynVCellMapper.SmoldynKeyword.cmd + " " + SmoldynVCellMapper.SmoldynKeyword.N + " " + n + " " + VCellSmoldynKeyword.vcellWriteOutput + " " + VCellSmoldynKeyword.dimension + " " + dimension);
printWriter.print(SmoldynVCellMapper.SmoldynKeyword.cmd + " " + SmoldynVCellMapper.SmoldynKeyword.N + " " + n + " " + VCellSmoldynKeyword.vcellWriteOutput + " " + VCellSmoldynKeyword.sampleSize + " " + sampleSize.getX());
if (dimension > 1) {
printWriter.print(" " + sampleSize.getY());
if (dimension > 2) {
printWriter.print(" " + sampleSize.getZ());
}
}
printWriter.println();
printWriter.println(SmoldynVCellMapper.SmoldynKeyword.cmd + " " + SmoldynVCellMapper.SmoldynKeyword.N + " " + n + " " + VCellSmoldynKeyword.vcellWriteOutput + " " + VCellSmoldynKeyword.numMembraneElements + " " + cartesianMesh.getNumMembraneElements());
for (ParticleVariable pv : particleVariableList) {
String type = pv instanceof MembraneParticleVariable ? VCellSmoldynKeyword.membrane.name() : VCellSmoldynKeyword.volume.name();
printWriter.println(SmoldynVCellMapper.SmoldynKeyword.cmd + " " + SmoldynVCellMapper.SmoldynKeyword.N + " " + n + " " + VCellSmoldynKeyword.vcellWriteOutput + " " + VCellSmoldynKeyword.variable + " " + pv.getName() + " " + type + " " + pv.getDomain().getName());
}
printWriter.println(SmoldynVCellMapper.SmoldynKeyword.cmd + " " + SmoldynVCellMapper.SmoldynKeyword.N + " " + n + " " + VCellSmoldynKeyword.vcellWriteOutput + " end");
} else {
throw new SolverException(SolverDescription.Smoldyn.getDisplayLabel() + " only supports uniform output.");
}
}
printWriter.println();
}
Also used :
ParticleInitialConditionConcentration(cbit.vcell.math.ParticleProperties.ParticleInitialConditionConcentration)
VolumeParticleVariable(cbit.vcell.math.VolumeParticleVariable)
MembraneParticleVariable(cbit.vcell.math.MembraneParticleVariable)
ParticleVariable(cbit.vcell.math.ParticleVariable)
ISize(org.vcell.util.ISize)
ProgrammingException(org.vcell.util.ProgrammingException)
GeometryException(cbit.vcell.geometry.GeometryException)
IOException(java.io.IOException)
DataAccessException(org.vcell.util.DataAccessException)
PropertyVetoException(java.beans.PropertyVetoException)
DivideByZeroException(cbit.vcell.parser.DivideByZeroException)
ImageException(cbit.image.ImageException)
ExpressionBindingException(cbit.vcell.parser.ExpressionBindingException)
SolverException(cbit.vcell.solver.SolverException)
ExpressionException(cbit.vcell.parser.ExpressionException)
MathException(cbit.vcell.math.MathException)
CompartmentSubDomain(cbit.vcell.math.CompartmentSubDomain)
SubDomain(cbit.vcell.math.SubDomain)
MembraneSubDomain(cbit.vcell.math.MembraneSubDomain)
TimeStep(cbit.vcell.solver.TimeStep)
OutputTimeSpec(cbit.vcell.solver.OutputTimeSpec)
UniformOutputTimeSpec(cbit.vcell.solver.UniformOutputTimeSpec)
MembraneParticleVariable(cbit.vcell.math.MembraneParticleVariable)
CompartmentSubDomain(cbit.vcell.math.CompartmentSubDomain)
ParticleInitialCondition(cbit.vcell.math.ParticleProperties.ParticleInitialCondition)
SolverException(cbit.vcell.solver.SolverException)
Aggregations
DivideByZeroException (cbit.vcell.parser.DivideByZeroException)4
Expression (cbit.vcell.parser.Expression)3
ExpressionException (cbit.vcell.parser.ExpressionException)2
DataAccessException (org.vcell.util.DataAccessException)2
ImageException (cbit.image.ImageException)1
PlotPane (cbit.plot.gui.PlotPane)1
FieldDataParameterVariable (cbit.vcell.field.FieldDataParameterVariable)1
GeometryException (cbit.vcell.geometry.GeometryException)1
CompartmentSubDomain (cbit.vcell.math.CompartmentSubDomain)1
MathException (cbit.vcell.math.MathException)1
MembraneParticleVariable (cbit.vcell.math.MembraneParticleVariable)1
MembraneSubDomain (cbit.vcell.math.MembraneSubDomain)1
ParticleInitialCondition (cbit.vcell.math.ParticleProperties.ParticleInitialCondition)1
ParticleInitialConditionConcentration (cbit.vcell.math.ParticleProperties.ParticleInitialConditionConcentration)1
ParticleVariable (cbit.vcell.math.ParticleVariable)1
ReservedVariable (cbit.vcell.math.ReservedVariable)1
SubDomain (cbit.vcell.math.SubDomain)1
VariableType (cbit.vcell.math.VariableType)1
VolumeParticleVariable (cbit.vcell.math.VolumeParticleVariable)1
ExpressionBindingException (cbit.vcell.parser.ExpressionBindingException)1
